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Blood samples from 489 unrelated Caucasian Mestizo and 252 individuals of African descent in Colombia were amplified and typed for three short tandem repeat (STR) markers (D12S1090, D3S1744, and D18S849). All markers conformed to Hardy-Weinberg equilibrium expectations in both populations studied. In addition, heterozygosity, mean exclusion chance, polymorphism information content, discrimination power, and the assumption of independence within and between loci were determined. The mean exclusion chance for all three STR markers is 0.9750 in the Caucasian Mestizo population and 0.9731 in the African Colombian Population. The discrimination power is 0.999925 and 0.999911 in the Caucasian Mestizo and African Colombian respectively.
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REFERENCE: Yunis JJ, Garcia O, Baena A, Arboleda G, Uriarte
I, and Yunis E. Population frequency for the short tandem repeat
loci D18S849, D3S1744, and D12S1090 in Caucasian-Mestizo and
African descent populations of Colombia. J Forensic Sci 2000;45
(2):429–431.
ABSTRACT: Blood samples from 489 unrelated Caucasian Mes-
tizo and 252 individuals of African descent in Colombia were am-
plified and typed for three short tandem repeat (STR) markers
(D12S1090, D3S1744, and D18S849). All markers conformed to
Hardy-Weinberg equilibrium expectations in both populations stud-
ied. In addition, heterozygosity, mean exclusion chance, polymor-
phism information content, discrimination power, and the assump-
tion of independence within and between loci were determined. The
mean exclusion chance for all three STR markers is 0.9750 in the
Caucasian Mestizo population and 0.9731 in the African Colombian
Population. The discrimination power is 0.999925 and 0.999911 in
the Caucasian Mestizo and African Colombian respectively.
KEYWORDS: forensic science, DNA typing, polymerase chain
reaction, short tandem repeats, population genetics, D12S1090,
D3S1744, D18S849, Colombia
In South America, few STR studies have been done for native,
Mestizo populations (1–3), and South American Black populations
(4), although many studies of STR profiles have been carried out for
the ancestral Spanish and Portuguese populations (5–9). Colombia
is a multi-ethnic and multi-cultural country with near 41 million
people composed of three ethnic groups (10), the Caucasian-Mes-
tizo population representing the largest group followed by the Black
population of African origin and the Amerindian populations (83
ethnic groups). The Caucasian-Mestizo population is composed of
Spanish descent and in a lesser extent of other European, Arabs and
Jewish populations among others and is located in the Andean re-
gion of Colombia and in a lesser extent in the Caribbean plains, Pa-
cific and Amazonian regions. The Black population is located in the
Pacific and Caribbean regions of the country (11,12). The ancestors
of the Black population of Colombia were brought as slaves from
the west coast of Guinea, Ivory Coast, Senegal, and Mali in Africa
to present day Colombia between 1580 and 1650 to work in the
fields and mines (13). By 1800, around 210,000 individuals of
African descent (14) were living in the country, in the Caribbean and
pacific coasts of Colombia. In 1993 a total of 502,343 individuals
(1.5% of the population) were counted (10) as Blacks.
We present the population frequencies of three polymorphic STR
loci analyzed in two major Colombian populations named
D12S1090 (n486 Caucasian-Mestizo; n248 Blacks),
D3S1744 (n484 Caucasian-Mestizo; n252 Blacks) and
D18S849 (n489 Caucasian Mestizo; n250 Blacks). The pop-
ulation frequencies obtained from these markers, not only are im-
portant for forensic science and paternity testing studies, but to char-
acterize genetically the Colombian population and sub-populations.
Materials and Methods
Whole blood was obtained from unrelated Caucasian-Mestizo
individuals from the Andean Region of Colombia requesting pa-
ternity testing studies and from unrelated individuals of African de-
scent collected in five different towns (around 50 individuals from
each town) of the Choco department in the Pacific region of
Colombia. Informed consent was obtained before drawing the
blood samples. The selection of the African descent individuals
was based on the fact that at least two generations did not have ad-
mixture with Caucasian or Amerindians based on interrogation at
the moment of the sample collection. None of these samples are
presumed to be from first-degree relatives.
Genomic DNA was isolated from whole blood by the Quick
Light DNA isolation kit (Lifecodes Corporation, Stamford, CT)
or by the Wizard Genomic DNA isolation kit (Promega Corpora-
tion, Madison, WI) following the manufacturer’s recommenda-
tions. The D12S1090, D3S1744, and D18S849 loci were ampli-
fied by PCR in a multiplex format using the Multiplex I kit
(Lifecodes Corporation, Stamford, CT) in a PTC100VG thermo-
cycler (MJ Research, Watertown, MA) following the manufactur-
ers protocols. The PCR products were resolved in a 4% Acryl-
429
TECHNICAL NOTE
Juan J. Yunis,
1,2
M.D.; Oscar Garcia,
3
M.Sc.; Andres Baena,
2
B.S.; Gonzalo Arboleda,
2
M.D.;
Ion Uriarte,
3
M.D.; and Emilio Yunis,
1
M.D.
Population Frequency for the Short Tandem
Repeat Loci D18S849, D3S1744, and D12S1090
in Caucasian-Mestizo and African Descent
Populations of Colombia
1
Servicios Medicos Yunis Turbay y Cia, Ave 22 #42–24, Santa Fé de Bo-
gota, Colombia.
2
Instituto de Genética, Universidad Nacional de Colombia, Santa Fé de Bo-
gotá, Colombia.
3
Area de Laboratorio Ertzaintza, C/ Avda. Montevideo 3, E-48002 Bilbao,
Spain.
Received 31 Dec. 1998; and in revised form 5 May 1999; accepted 25 June
1999.
Copyright © 2000 by ASTM International
430 JOURNAL OF FORENSIC SCIENCES
amide-Bis-Acrylamide denaturing gel at 2000 V/1 h and detected
by silver nitrate staining (15) and manually interpreted by two
persons. Allele designations were based on the allelic ladder pro-
vided by the manufacturer.
Statistical evaluations were performed using the HWE-Analysis
software package (HWE-Analysis, Version 3.3. Christoph Puers,
Institute of Legal Medicine, University of Münster). Analyses in-
cluded the possible divergence from Hardy-Weinberg expectations
and other parameters of forensic importance: observed and ex-
pected heterozygosity (16), mean exclusion chance (MEC) (17),
mean paternity exclusion probability (MEP) (18), polymorphic in-
formation content (PIC) (19), and discrimination power (DP) (20).
In addition the GDA computer program (Lewis, P.O., Zaykin,
D. 1999. Genetic Data Analysis. Computer program for the analy-
sis of allelic data. Version 1.0 (d12), free program distributed
by the authors over the internet from the GDA Home Page at
http//chee.unm.edu /gda/), was used to analyze the possible associ-
ations between loci.
Results and Discussion
Table 1 shows the allele frequency distribution for D12S1090,
D3S1744, and D18S849 in the Caucasian-Mestizo and African de-
scent individuals of Colombia. In addition, minimum allele frequen-
cies for PCR based loci based on statistical and populations genetics
theory were determined (21–23) (Table 1). Therefore, a greater con-
fidence with current size databases can be attained for DNA profile
frequency estimates in forensic casework. Also, the results of the dif-
ferent test procedures to determine the correspondence of the geno-
type frequencies with their Hardy-Weinberg equilibrium are shown.
All markers were found to be in HW equilibrium by all three test
used (X
2
-test, the logarithmic likelihood ratio (G test) and exact test)
(24). An interclass correlation test analysis demonstrated that there is
no evidence of associations between any pair of loci in any of these
two populations (data not shown), as should be expected when inde-
pendent loci in different chromosomes are analyzed.
To evaluate the differences between these two populations, a R
C contingency table was used (data not shown). The allele fre-
quency distribution for locus D3S1744 did not show any statistical
significant difference between these two populations (0.1 p
0.2). Statistical significant differences were detected for locus
D12S1090 and D18S849 (p0.0005). A similar comparison (data
not shown) was carried out between the Colombian Caucasian
Mestizo population and the USA Caucasian population, between
the Colombian Caucasian Mestizo and the USA Hispanics (re-
ported by the manufacturer) and between Black population from
Colombia and Blacks from the USA (17) showing no statistically
significant differences between them.
No statistical significant differences were observed when R C
tables were used to compare the data obtained from the five differ-
ent towns of the Choco department sampled despite the low num-
ber of individuals analyzed (data not shown). This findings could
TABLE 1—Observed allele frequencies and tests for Hardy-Weinberg equilibrium for D18S849, D3S1744, and D12S1090 loci, in Caucasian-Mestizos
and Black individuals from Colombia.
Caucasian Caucasian Caucasian
Mestizo Mestizo Mestizo Blacks Blacks Blacks
n489 n484 n486 n250 n252 n248
Allele D18S849 D3S1744 D12S1090 D18S849 D3S1744 D12S1090
9 0.001 0.069 0.062 0.022
10 0.017 0.010
11 0.001 0.053 0.004 0.057
12 0.003 0.063 0.016 0.111
13 0.010 0.034 0.006 0.036
14 0.048 0.004 0.045 0.020 0.002 0.042
15 0.212 0.096 0.012 0.218 0.066 0.012
16 0.408 0.084 0.006 0.390 0.089 0.002
17 0.197 0.142 0.004 0.192 0.173 0.012
18 0.095 0.367 0.018 0.086 0.365 0.020
19 0.022 0.173 0.055 0.006 0.175 0.050
20 0.003 0.101 0.083 0.079 0.099
21 0.027 0.076 0.042 0.093
22 0.007 0.108 0.006 0.119
23 0.066 0.004 0.061
24 0.066 0.034
25 0.058 0.057
26 0.077 0.046
27 0.060 0.038
28 0.011 0.008
29 0.012 0.032
30 0.007 0.020
31 0.012
32 0.001 0.002
33 0.004
Frec.min 0.006 0.006 0.007 0.011 0.012 0.014
HET obs. 26 29 141 23 27 116
HET EX. SE. 24.34 4.31 27.33 3.46 144.37 10.91 23.11 4.41 24.95 3.84 114.78 12.72
Homo obs. 5 6 14 5 6 9
Homo EX. SE 4.93 1.31 6.28 1.06 12.07 2.91 4.63 1.43 5.69 1.69 8.18 3.35
X
2
test 0.147 0.200 0.463 0.908 0.939 0.377
G test 0.116 0.196 0.412 0.931 0.923 0.148
Exact test 0.055 0.118 0.472 0.952 0.802 0.127
be due in part to a process of genetic “homogenization” carried out
by the slavers in Colombia (13). In that process, individuals speak-
ing the same language were separated in order to avoid emancipa-
tion movements among the slaves. A similar result was obtained
comparing Black populations of Brazil and Venezuela (4). This ad-
mixture process will limit the usefulness of STR markers to trace
back the origin of the Colombian Black population with their spe-
cific African ancestors.
Table 2 shows several parameters of statistical importance for
the loci studied in the Caucasian Mestizo and Black populations of
Colombia such as observed and expected heterozygosity, mean ex-
clusion chance (MEC), mean paternity exclusion (MEP), polymor-
phic information content (PIC) and discrimination power (DP).
Similar results were obtained in both populations for the observed
heterozygosity, MEC, and DP.
In summary, the population frequency of Caucasian-Mestizo
and African Colombians has been established for STR loci
D12S1090, D3S1744, and D18S849. All STR loci were found to be
in HW equilibrium. The combined power of exclusion is estimated
as 0.9750 in the Caucasian Mestizo and 0.9731 in the African
Colombian population. The results obtained in this study can be
used to derive estimates of multiple loci profiles frequencies for
forensic purposes, to calculate paternity indexes and the probabil-
ity of paternity in parentage testing studies and to genetically char-
acterize the Colombian population in population studies.
Acknowledgments
We would like to thank Sandra P. Moreno, Martha Roa, and
Yolanda Gonzalez for their technical assistance.
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Additional information and reprint requests:
Juan J. Yunis, M.D.
Profesor Asociado
Instituto de Genética
Universidad Nacional de Colombia
Santa Fé de Bogotá, Colombia.
YUNIS ET AL. POPULATION FREQUENCY 431
TABLE 2—Statistical parameters of forensic importance for D12S1090, D3S1744, and D18S849 loci in Caucasian Mestizo and Blacks from Colombia.
Caucasian Caucasian Caucasian
Mestizo Mestizo Mestizo Blacks Blacks Blacks
Locus D18S849 D3S1744 D12S1090 D18S849 D3S1744 D12S1090
HET obs 0.714 0.775 0.930 0.732 0.774 0.944
MEC 0.519 0.604 0.869 0.539 0.599 0.862
MEP 0.491 0.579 0.870 0.515 0.576 0.865
PIC 0.701 0.763 0.932 0.717 0.760 0.928
DP 0.892 0.929 0.990 0.908 0.927 0.987
Caucasian Mestizo Blacks
MEC Total 0.9750 0.9731
DP total 0.999925 0.999911
... Thus, the genetic pool was limited to male European Caucasians and Amerindian mtDNA. This admixture process would have generated the Caucasian/ Amerindian sex bias based on Y-Chromosomes and mtDNA, as mentioned earlier, but with various degrees of admixture at the autosomal level which differentiates the present day population from the Amerindian and Spanish populations, as it has been demonstrated for the Caucasian-mestizo population of Colombia and different populations from Spain and Portugal, based on autosomic STR analysis (43)(44)(45). In that regard, in another report (26), the analysis of 305 unrelated individuals from the departments located in the Caribbean region of Colombia showed that most of the Y-chromosome haplotypes present in that region of the country, are also of Spanish/European origin that clustered near the populations reported by us and others published in YHRD database. ...
... On the other hand, our sample seems to be genetically distant from the Basque population, a result likely due to the fact that the Basque immigrants to present day Colombia are mainly located in the west section of the country(47).The African descent population clustered with other African descent populations such as the African-American and the population from Surinam. Based on autosomal STR analyzed for the African descent population of Colombia(43)(44)(45) no statistically significant differences were found with the African American population. Our results with Y-STR haplotypes are in agreement with our previous findings, as well as historical data suggesting a common origin in the West coast of Africa for both the African American and Afro-Colombian individuals. ...
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... Thus, the genetic pool was limited to male European Caucasians and Amerindian mtDNA. This admixture process would have generated the Caucasian/ Amerindian sex bias based on Y-Chromosomes and mtDNA, as mentioned earlier, but with various degrees of admixture at the autosomal level which differentiates the present day population from the Amerindian and Spanish populations, as it has been demonstrated for the Caucasian-mestizo population of Colombia and different populations from Spain and Portugal, based on autosomic STR analysis (43)(44)(45). In that regard, in another report (26), the analysis of 305 unrelated individuals from the departments located in the Caribbean region of Colombia showed that most of the Y-chromosome haplotypes present in that region of the country, are also of Spanish/European origin that clustered near the populations reported by us and others published in YHRD database. ...
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... Amerindians (3.4%) and gypsies (0.1%). Spaniards represent the main Caucasian ancestral population that arrived soon after the discovery of America by Columbus in 1492 (Sandoval et al., 1993;Mesa et al., 2000;Yunis et al., 2000aYunis et al., , 2005aSalas et al., 2008). Other Europeans (German, Italian and French, among others) as well as Arab and Jewish populations have also contributed to the admixture in different regions of present-day Colombia (Yunis et al., 2000a(Yunis et al., , 2005a. ...
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